Yes the
Cupra turned into the FR around October 2004 I believe (around the changeover point you can actually get cars with both FR badges on the wings and a
Cupra badge on the rear!). Basically the same car with a few aesthetic differences as strugers1 said (although I didn't know the seats were different).
Also the
Cupra had the CD changer in the glovebox as standard, whereas it was an option on the FR.
Also the last of the FRs are known as the FR+ and have
Cupra R bumpers and 17" versions of the
Cupra R alloys, and the "F" in the
badge is red as well as the "R".
Which is the better car basically depends upon which you think looks the best. In my opinion it's FR+, FR then
Cupra.